Chapter 5 Compositional analysis
load("data/data_podarcis_filfolensis.Rdata")
load("data/data_podarcis_gaigeae.Rdata")
load("data/data_podarcis_milensis.Rdata")
load("data/data_podarcis_pityusensis.Rdata")
load("data/data_podarcis_all.Rdata")5.1 Taxonomy barplots
5.1.1 Podarcis filfolensis
genome_counts_filt_pf %>%
mutate_at(vars(-genome),~./sum(.)) %>% #apply TSS nornalisation
pivot_longer(-genome, names_to = "sample", values_to = "count") %>% #reduce to minimum number of columns
left_join(., genome_metadata_pf, by = join_by(genome == genome)) %>% #append genome metadata
left_join(., sample_metadata_pf, by = join_by(sample == sample)) %>% #append sample metadata
filter(!is.na(count)) %>%
ggplot(aes(y=count,x=sample, fill=phylum, group=phylum)) + #grouping enables keeping the same sorting of taxonomic units
geom_bar(stat="identity", colour="white", linewidth=0.1) + #plot stacked bars with white borders
scale_fill_manual(values=phylum_colors_pf) +
labs(x = "Relative abundance", y ="Samples") +
facet_nested(. ~ population, scales="free", space="free") + #facet per day and treatment
scale_y_continuous(expand = c(0.001, 0.001)) +
theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1),
axis.title.x = element_blank(),
panel.background = element_blank(),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
axis.line = element_line(linewidth = 0.5, linetype = "solid", colour = "black"),
legend.position = "none",
strip.background.x=element_rect(color = NA, fill= "#f4f4f4"))genome_counts_filt_pg %>%
mutate_at(vars(-genome),~./sum(.)) %>% #apply TSS nornalisation
pivot_longer(-genome, names_to = "sample", values_to = "count") %>% #reduce to minimum number of columns
left_join(., genome_metadata_pg, by = join_by(genome == genome)) %>% #append genome metadata
left_join(., sample_metadata_pg, by = join_by(sample == sample)) %>% #append sample metadata
filter(!is.na(count)) %>%
ggplot(aes(y=count,x=sample, fill=phylum, group=phylum)) + #grouping enables keeping the same sorting of taxonomic units
geom_bar(stat="identity", colour="white", linewidth=0.1) + #plot stacked bars with white borders
scale_fill_manual(values=phylum_colors_pg) +
labs(x = "Relative abundance", y ="Samples") +
facet_nested(. ~ population, scales="free", space="free") + #facet per day and treatment
scale_y_continuous(expand = c(0.001, 0.001)) +
theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1),
axis.title.x = element_blank(),
panel.background = element_blank(),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
axis.line = element_line(linewidth = 0.5, linetype = "solid", colour = "black"),
legend.position = "none",
strip.background.x=element_rect(color = NA, fill= "#f4f4f4"))genome_counts_filt_pm %>%
mutate_at(vars(-genome),~./sum(.)) %>% #apply TSS nornalisation
pivot_longer(-genome, names_to = "sample", values_to = "count") %>% #reduce to minimum number of columns
left_join(., genome_metadata_pm, by = join_by(genome == genome)) %>% #append genome metadata
left_join(., sample_metadata_pm, by = join_by(sample == sample)) %>% #append sample metadata
filter(!is.na(count)) %>%
ggplot(aes(y=count,x=sample, fill=phylum, group=phylum)) + #grouping enables keeping the same sorting of taxonomic units
geom_bar(stat="identity", colour="white", linewidth=0.1) + #plot stacked bars with white borders
scale_fill_manual(values=phylum_colors_pm) +
labs(x = "Relative abundance", y ="Samples") +
facet_nested(. ~ population, scales="free", space="free") + #facet per day and treatment
scale_y_continuous(expand = c(0.001, 0.001)) +
theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1),
axis.title.x = element_blank(),
panel.background = element_blank(),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
axis.line = element_line(linewidth = 0.5, linetype = "solid", colour = "black"),
legend.position = "none",
strip.background.x=element_rect(color = NA, fill= "#f4f4f4"))genome_counts_filt_pp %>%
mutate_at(vars(-genome),~./sum(.)) %>% #apply TSS nornalisation
pivot_longer(-genome, names_to = "sample", values_to = "count") %>% #reduce to minimum number of columns
left_join(., genome_metadata_pp, by = join_by(genome == genome)) %>% #append genome metadata
left_join(., sample_metadata_pp, by = join_by(sample == sample)) %>% #append sample metadata
filter(!is.na(count)) %>%
ggplot(aes(y=count,x=sample, fill=phylum, group=phylum)) + #grouping enables keeping the same sorting of taxonomic units
geom_bar(stat="identity", colour="white", linewidth=0.1) + #plot stacked bars with white borders
scale_fill_manual(values=phylum_colors_pp) +
labs(x = "Relative abundance", y ="Samples") +
facet_nested(. ~ population, scales="free", space="free") + #facet per day and treatment
scale_y_continuous(expand = c(0.001, 0.001)) +
theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1),
axis.title.x = element_blank(),
panel.background = element_blank(),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
axis.line = element_line(linewidth = 0.5, linetype = "solid", colour = "black"),
legend.position = "none",
strip.background.x=element_rect(color = NA, fill= "#f4f4f4"))5.2 Taxonomic representation
5.2.1 Phylum
phylum_summary <- genome_counts_filt_all %>%
mutate_at(vars(-genome),~./sum(.)) %>% #apply TSS nornalisation
pivot_longer(-genome, names_to = "sample", values_to = "count") %>% #reduce to minimum number of columns
left_join(sample_metadata_all, by = join_by(sample == sample)) %>% #append sample metadata
left_join(genome_metadata_all, by = join_by(genome == genome)) %>% #append genome metadata
group_by(sample,phylum) %>%
summarise(relabun=sum(count))
phylum_summary %>%
filter(!is.na(relabun)) %>%
group_by(phylum) %>%
summarise(mean=mean(relabun),sd=sd(relabun)) %>%
mutate(phylum= sub("^p__", "", phylum)) %>%
arrange(-mean) %>%
tt()| phylum | mean | sd |
|---|---|---|
| Bacillota_A | 4.355073e-01 | 0.1637303694 |
| Bacteroidota | 3.795311e-01 | 0.1493442024 |
| Bacillota | 6.693929e-02 | 0.0613238855 |
| Pseudomonadota | 4.237993e-02 | 0.0659965403 |
| Desulfobacterota | 1.762937e-02 | 0.0168493333 |
| Campylobacterota | 1.394838e-02 | 0.0229133933 |
| Cyanobacteriota | 8.474584e-03 | 0.0120549930 |
| Verrucomicrobiota | 8.226209e-03 | 0.0140684507 |
| Bacillota_C | 6.505350e-03 | 0.0077147585 |
| Spirochaetota | 5.445050e-03 | 0.0249843346 |
| Bacillota_B | 4.111308e-03 | 0.0057340543 |
| Fusobacteriota | 3.024136e-03 | 0.0134489815 |
| Halobacteriota | 2.947999e-03 | 0.0105666272 |
| Actinomycetota | 2.221294e-03 | 0.0190806008 |
| Chlamydiota | 1.109162e-03 | 0.0112564276 |
| Elusimicrobiota | 1.104802e-03 | 0.0036746035 |
| Synergistota | 3.666072e-04 | 0.0024311729 |
| Planctomycetota | 1.908305e-04 | 0.0017144286 |
| 1.473864e-04 | 0.0009299590 | |
| Deferribacterota | 1.413909e-04 | 0.0006340007 |
| Thermoplasmatota | 4.851518e-05 | 0.0006362706 |
phylum_arrange <- phylum_summary %>%
filter(!is.na(relabun)) %>%
group_by(phylum) %>%
summarise(mean=sum(relabun)) %>%
arrange(-mean) %>%
select(phylum) %>%
#mutate(phylum= sub("^p__", "", phylum)) %>%
pull()
phylum_summary %>%
left_join(genome_metadata_all %>% select(phylum) %>% unique(),by="phylum") %>%
left_join(sample_metadata_all,by=join_by(sample==sample)) %>%
filter(phylum != "p__") %>%
#mutate(phylum= sub("^p__", "", phylum)) %>%
filter(phylum %in% phylum_arrange[1:20]) %>%
mutate(phylum=factor(phylum,levels=rev(phylum_arrange[1:20]))) %>%
filter(relabun > 0) %>%
ggplot(aes(x=relabun, y=phylum, group=phylum, color=phylum, fill=phylum)) +
scale_color_manual(values=phylum_colors_all) +
scale_fill_manual(values=phylum_colors_all) +
geom_jitter(alpha=0.5) +
facet_nested(. ~ species)+
theme_minimal() +
theme(legend.position = "none")5.2.2 Order
order_summary <- genome_counts_filt_all %>%
mutate_at(vars(-genome),~./sum(.)) %>% #apply TSS nornalisation
pivot_longer(-genome, names_to = "sample", values_to = "count") %>% #reduce to minimum number of columns
left_join(sample_metadata_all %>% rename(host_order=order), by = join_by(sample == sample)) %>% #append sample metadata
left_join(genome_metadata_all, by = join_by(genome == genome)) %>% #append genome metadata
group_by(sample,order) %>%
summarise(relabun=sum(count))
order_summary %>%
filter(!is.na(relabun)) %>%
group_by(order) %>%
summarise(mean=mean(relabun),sd=sd(relabun)) %>%
mutate(famorderily= sub("^o__", "", order)) %>%
arrange(-mean) %>%
tt()| order | mean | sd | famorderily |
|---|---|---|---|
| o__Bacteroidales | 3.795311e-01 | 0.1493442024 | Bacteroidales |
| o__Lachnospirales | 2.817732e-01 | 0.1573578010 | Lachnospirales |
| o__Oscillospirales | 7.730821e-02 | 0.0482442135 | Oscillospirales |
| o__Christensenellales | 6.152228e-02 | 0.0521531204 | Christensenellales |
| o__Erysipelotrichales | 3.205759e-02 | 0.0472082321 | Erysipelotrichales |
| o__Desulfovibrionales | 1.762937e-02 | 0.0168493333 | Desulfovibrionales |
| o__Enterobacterales | 1.596443e-02 | 0.0397310018 | Enterobacterales |
| o__Campylobacterales | 1.394838e-02 | 0.0229133933 | Campylobacterales |
| o__Mycoplasmatales | 9.674457e-03 | 0.0201025198 | Mycoplasmatales |
| o__Acholeplasmatales | 9.244018e-03 | 0.0156078657 | Acholeplasmatales |
| o__Gastranaerophilales | 8.474584e-03 | 0.0120549930 | Gastranaerophilales |
| o__RF32 | 7.907507e-03 | 0.0109564629 | RF32 |
| o__RF39 | 7.616380e-03 | 0.0129867266 | RF39 |
| o__Verrucomicrobiales | 7.557137e-03 | 0.0136890242 | Verrucomicrobiales |
| o__Enterobacterales_A | 6.146616e-03 | 0.0225932402 | Enterobacterales_A |
| o__RFN20 | 5.491908e-03 | 0.0134551586 | RFN20 |
| o__TANB77 | 5.387227e-03 | 0.0091071005 | TANB77 |
| o__Peptostreptococcales | 4.806343e-03 | 0.0075471530 | Peptostreptococcales |
| o__UBA3830 | 4.368400e-03 | 0.0098939122 | UBA3830 |
| o__Clostridiales | 4.071744e-03 | 0.0181994301 | Clostridiales |
| o__Selenomonadales | 3.953551e-03 | 0.0066974902 | Selenomonadales |
| o__Peptococcales | 3.689298e-03 | 0.0055754286 | Peptococcales |
| o__Sphaerochaetales | 3.529054e-03 | 0.0216011752 | Sphaerochaetales |
| o__Diplorickettsiales | 3.505108e-03 | 0.0459055178 | Diplorickettsiales |
| o__Fusobacteriales | 3.024136e-03 | 0.0134489815 | Fusobacteriales |
| o__Acidaminococcales | 2.551799e-03 | 0.0049055131 | Acidaminococcales |
| o__Methanosarcinales | 2.372541e-03 | 0.0097274543 | Methanosarcinales |
| o__RUG11792 | 2.184233e-03 | 0.0053494956 | RUG11792 |
| o__Actinomycetales | 1.561179e-03 | 0.0190765399 | Actinomycetales |
| o__Lactobacillales | 1.265853e-03 | 0.0051617233 | Lactobacillales |
| o__Chlamydiales | 1.109162e-03 | 0.0112564276 | Chlamydiales |
| o__Elusimicrobiales | 1.104802e-03 | 0.0036746035 | Elusimicrobiales |
| o__ML615J-28 | 9.826848e-04 | 0.0037803511 | ML615J-28 |
| o__Brevinematales | 8.957611e-04 | 0.0046437768 | Brevinematales |
| o__GWE2-31-10 | 8.620607e-04 | 0.0040717621 | GWE2-31-10 |
| o__Coriobacteriales | 6.601149e-04 | 0.0013420095 | Coriobacteriales |
| o__CAJFEE01 | 6.063947e-04 | 0.0028904690 | CAJFEE01 |
| o__Methanomicrobiales | 5.754579e-04 | 0.0026410958 | Methanomicrobiales |
| o__ | 5.717583e-04 | 0.0021241114 | |
| o__Rs-D84 | 5.603757e-04 | 0.0031715201 | Rs-D84 |
| o__Rickettsiales | 5.287290e-04 | 0.0027549629 | Rickettsiales |
| o__UBA1381 | 5.035832e-04 | 0.0015475012 | UBA1381 |
| o__Opitutales | 4.901270e-04 | 0.0018532230 | Opitutales |
| o__Synergistales | 3.666072e-04 | 0.0024311729 | Synergistales |
| o__Pseudomonadales | 3.626249e-04 | 0.0029135461 | Pseudomonadales |
| o__UBA7702 | 2.450743e-04 | 0.0015747068 | UBA7702 |
| o__Cardiobacteriales | 2.276453e-04 | 0.0029855408 | Cardiobacteriales |
| o__Pirellulales | 1.908305e-04 | 0.0017144286 | Pirellulales |
| o__Victivallales | 1.789455e-04 | 0.0015054509 | Victivallales |
| o__UBA4068 | 1.769355e-04 | 0.0005665926 | UBA4068 |
| o__Burkholderiales | 1.721286e-04 | 0.0007779434 | Burkholderiales |
| o__Treponematales | 1.581747e-04 | 0.0008279556 | Treponematales |
| o__Deferribacterales | 1.413909e-04 | 0.0006340007 | Deferribacterales |
| o__UMGS1883 | 7.335614e-05 | 0.0004670412 | UMGS1883 |
| o__Methanomassiliicoccales | 4.851518e-05 | 0.0006362706 | Methanomassiliicoccales |
| o__Eubacteriales | 3.408400e-05 | 0.0001552477 | Eubacteriales |
| o__Rhodobacterales | 2.776073e-05 | 0.0003101775 | Rhodobacterales |
| o__Tissierellales | 2.729052e-05 | 0.0003579118 | Tissierellales |
order_arrange <- order_summary %>%
filter(!is.na(relabun)) %>%
group_by(order) %>%
summarise(mean=sum(relabun)) %>%
arrange(-mean) %>%
select(order) %>%
mutate(order= sub("^o__", "", order)) %>%
pull()
order_summary %>%
left_join(genome_metadata_all %>% select(order,phylum) %>% unique(),by="order") %>%
left_join(sample_metadata_all %>% rename(host_order=order),by="sample") %>%
filter(order != "o__") %>%
mutate(order= sub("^o__", "", order)) %>%
filter(order %in% order_arrange[1:20]) %>%
mutate(order=factor(order,levels=rev(order_arrange[1:20]))) %>%
filter(relabun > 0) %>%
ggplot(aes(x=relabun, y=order, group=order, color=phylum, fill=phylum)) +
scale_color_manual(values=phylum_colors_all) +
scale_fill_manual(values=phylum_colors_all) +
#geom_boxplot(alpha=0.2) +
geom_jitter(alpha=0.5) +
facet_nested(. ~ species)+
theme_minimal() +
theme(legend.position = "none")5.2.3 Family
family_summary <- genome_counts_filt_all %>%
mutate_at(vars(-genome),~./sum(.)) %>% #apply TSS nornalisation
pivot_longer(-genome, names_to = "sample", values_to = "count") %>% #reduce to minimum number of columns
left_join(sample_metadata_all, by = join_by(sample == sample)) %>% #append sample metadata
left_join(genome_metadata_all, by = join_by(genome == genome)) %>% #append genome metadata
group_by(sample,family) %>%
summarise(relabun=sum(count))
family_summary %>%
filter(!is.na(relabun)) %>%
group_by(family) %>%
summarise(mean=mean(relabun),sd=sd(relabun)) %>%
mutate(family= sub("^f__", "", family)) %>%
arrange(-mean) %>%
tt()| family | mean | sd |
|---|---|---|
| Lachnospiraceae | 2.679049e-01 | 1.479098e-01 |
| Bacteroidaceae | 2.128971e-01 | 1.133002e-01 |
| Tannerellaceae | 7.843675e-02 | 4.086968e-02 |
| Rikenellaceae | 4.521289e-02 | 3.594946e-02 |
| Marinifilaceae | 3.815762e-02 | 3.130093e-02 |
| Ruminococcaceae | 3.516717e-02 | 2.681469e-02 |
| UBA3700 | 3.100225e-02 | 3.669198e-02 |
| Oscillospiraceae | 2.542478e-02 | 2.063380e-02 |
| Erysipelotrichaceae | 2.220306e-02 | 3.495105e-02 |
| 1.854607e-02 | 2.537000e-02 | |
| Desulfovibrionaceae | 1.762937e-02 | 1.684933e-02 |
| Enterobacteriaceae | 1.596443e-02 | 3.973100e-02 |
| Helicobacteraceae | 1.394838e-02 | 2.291339e-02 |
| Acutalibacteraceae | 1.129138e-02 | 2.182770e-02 |
| Coprobacillaceae | 9.854533e-03 | 1.610175e-02 |
| Mycoplasmoidaceae | 9.198005e-03 | 1.988191e-02 |
| Pumilibacteraceae | 8.303712e-03 | 2.717791e-02 |
| UBA660 | 7.616380e-03 | 1.298673e-02 |
| Akkermansiaceae | 7.557137e-03 | 1.368902e-02 |
| CAG-239 | 7.371042e-03 | 9.989587e-03 |
| Gastranaerophilaceae | 7.216239e-03 | 1.061888e-02 |
| Anaerotignaceae | 6.013824e-03 | 8.783101e-03 |
| Anaeroplasmataceae | 5.687338e-03 | 1.422618e-02 |
| Butyricicoccaceae | 5.289808e-03 | 6.576968e-03 |
| CAG-74 | 4.607693e-03 | 1.032186e-02 |
| CAG-508 | 4.495099e-03 | 8.141235e-03 |
| Anaerovoracaceae | 4.441054e-03 | 7.271621e-03 |
| Vibrionaceae | 4.421724e-03 | 1.848524e-02 |
| Clostridiaceae | 4.071744e-03 | 1.819943e-02 |
| DTU072 | 3.904841e-03 | 7.233438e-03 |
| Peptococcaceae | 3.689298e-03 | 5.575429e-03 |
| CAG-449 | 3.598003e-03 | 1.246597e-02 |
| Sphaerochaetaceae | 3.529054e-03 | 2.160118e-02 |
| WRBM01 | 3.523614e-03 | 6.291393e-03 |
| Diplorickettsiaceae | 3.505108e-03 | 4.590552e-02 |
| UBA932 | 3.368690e-03 | 8.602302e-03 |
| Fusobacteriaceae | 3.024136e-03 | 1.344898e-02 |
| CAG-917 | 2.786813e-03 | 1.051273e-02 |
| Acidaminococcaceae | 2.551799e-03 | 4.905513e-03 |
| Methanosarcinaceae | 2.372541e-03 | 9.727454e-03 |
| Borkfalkiaceae | 2.215945e-03 | 9.726245e-03 |
| UBA1242 | 1.975129e-03 | 4.034220e-03 |
| CAG-274 | 1.901813e-03 | 4.757881e-03 |
| Aeromonadaceae | 1.724892e-03 | 1.089339e-02 |
| CAG-288 | 1.623242e-03 | 5.036122e-03 |
| Micrococcaceae | 1.546507e-03 | 1.907650e-02 |
| MGBC116941 | 1.403668e-03 | 4.908522e-03 |
| CALTSX01 | 1.109162e-03 | 1.125643e-02 |
| Elusimicrobiaceae | 1.104802e-03 | 3.674604e-03 |
| CAG-314 | 1.067128e-03 | 3.487523e-03 |
| CAG-138 | 1.028579e-03 | 6.324693e-03 |
| CALVMC01 | 9.864994e-04 | 3.349719e-03 |
| RUG14156 | 9.300233e-04 | 2.736356e-03 |
| UBA3830 | 9.142222e-04 | 2.758943e-03 |
| Brevinemataceae | 8.957611e-04 | 4.643777e-03 |
| GWE2-31-10 | 8.620607e-04 | 4.071762e-03 |
| Eggerthellaceae | 6.601149e-04 | 1.342009e-03 |
| CAJFEE01 | 6.063947e-04 | 2.890469e-03 |
| Methanocorpusculaceae | 5.754579e-04 | 2.641096e-03 |
| Rs-D84 | 5.603757e-04 | 3.171520e-03 |
| Muribaculaceae | 5.226674e-04 | 3.051788e-03 |
| CAG-313 | 5.117558e-04 | 2.193878e-03 |
| UBA1381 | 5.035832e-04 | 1.547501e-03 |
| LL51 | 4.763559e-04 | 1.852608e-03 |
| CAG-698 | 4.709290e-04 | 2.164469e-03 |
| UBA1997 | 4.208195e-04 | 2.382923e-03 |
| Streptococcaceae | 4.160441e-04 | 2.630200e-03 |
| Enterococcaceae | 4.090411e-04 | 1.517990e-03 |
| CAG-465 | 3.788372e-04 | 1.164817e-03 |
| Coprobacteraceae | 3.767262e-04 | 1.347094e-03 |
| Synergistaceae | 3.666072e-04 | 2.431173e-03 |
| Peptostreptococcaceae | 3.652882e-04 | 1.348669e-03 |
| Pseudomonadaceae | 3.626249e-04 | 2.913546e-03 |
| Massilibacillaceae | 3.253008e-04 | 1.474960e-03 |
| UBA3637 | 3.139388e-04 | 1.531614e-03 |
| Metamycoplasmataceae | 3.110466e-04 | 3.810180e-03 |
| CHK158-818 | 3.095362e-04 | 9.740463e-04 |
| CAG-631 | 2.706635e-04 | 1.015132e-03 |
| Lactobacillaceae | 2.576707e-04 | 2.262342e-03 |
| UBA7702 | 2.450743e-04 | 1.574707e-03 |
| Wohlfahrtiimonadaceae | 2.276453e-04 | 2.985541e-03 |
| CAG-977 | 2.225261e-04 | 1.355731e-03 |
| SIG350 | 2.069507e-04 | 2.714132e-03 |
| Thermoguttaceae | 1.908305e-04 | 1.714429e-03 |
| CAJFVJ01 | 1.892159e-04 | 1.389700e-03 |
| Burkholderiaceae | 1.721286e-04 | 7.779434e-04 |
| Hepatoplasmataceae | 1.654048e-04 | 1.179092e-03 |
| Treponemataceae | 1.581747e-04 | 8.279556e-04 |
| UBA5755 | 1.525827e-04 | 5.351000e-04 |
| Mucispirillaceae | 1.413909e-04 | 6.340007e-04 |
| UBA1234 | 1.381659e-04 | 5.154643e-04 |
| Catellicoccaceae | 9.608682e-05 | 8.591908e-04 |
| CAG-272 | 9.588815e-05 | 7.206419e-04 |
| Vagococcaceae | 8.701072e-05 | 1.141135e-03 |
| Victivallaceae | 7.718385e-05 | 4.488404e-04 |
| Azobacteroidaceae | 7.440778e-05 | 9.758489e-04 |
| UMGS1883 | 7.335614e-05 | 4.670412e-04 |
| Cellulosilyticaceae | 5.332328e-05 | 3.808652e-04 |
| Methanomethylophilaceae | 4.851518e-05 | 6.362706e-04 |
| DUVY01 | 4.637858e-05 | 5.673763e-04 |
| Paludibacteraceae | 4.504653e-05 | 2.212459e-04 |
| CAG-382 | 3.918633e-05 | 1.936551e-04 |
| Eubacteriaceae | 3.408400e-05 | 1.552477e-04 |
| JAEDCM01 | 3.306564e-05 | 4.336518e-04 |
| Rhodobacteraceae | 2.776073e-05 | 3.101775e-04 |
| Peptoniphilaceae | 2.729052e-05 | 3.579118e-04 |
| HGM11417 | 2.626128e-05 | 1.876693e-04 |
| UBA4068 | 2.435275e-05 | 9.859687e-05 |
| Microbacteriaceae | 1.467237e-05 | 1.924263e-04 |
| UBA9783 | 1.377110e-05 | 1.243972e-04 |
| WCHB1-69 | 5.663380e-06 | 7.427454e-05 |
family_arrange <- family_summary %>%
filter(!is.na(relabun)) %>%
group_by(family) %>%
summarise(mean=sum(relabun)) %>%
arrange(-mean) %>%
select(family) %>%
mutate(family= sub("^f__", "", family)) %>%
pull()
family_summary %>%
left_join(genome_metadata_all %>% select(family,phylum) %>% unique(),by=join_by(family==family)) %>%
left_join(sample_metadata_all,by=join_by(sample==sample)) %>%
filter(family != "f__") %>%
mutate(family= sub("^f__", "", family)) %>%
filter(family %in% family_arrange[1:20]) %>%
mutate(family=factor(family,levels=rev(family_arrange[1:20]))) %>%
filter(relabun > 0) %>%
ggplot(aes(x=relabun, y=family, group=family, color=phylum, fill=phylum)) +
scale_color_manual(values=phylum_colors_all) +
scale_fill_manual(values=phylum_colors_all) +
#geom_boxplot(alpha=0.2) +
geom_jitter(alpha=0.5) +
facet_nested(. ~ species)+
theme_minimal() +
theme(legend.position = "none")5.2.4 Genus
genus_summary <- genome_counts_filt_all %>%
mutate_at(vars(-genome),~./sum(.)) %>% #apply TSS nornalisation
pivot_longer(-genome, names_to = "sample", values_to = "count") %>% #reduce to minimum number of columns
left_join(sample_metadata_all, by = join_by(sample == sample)) %>% #append sample metadata
left_join(genome_metadata_all, by = join_by(genome == genome)) %>% #append genome metadata
group_by(sample,genus) %>%
summarise(relabun=sum(count)) %>%
filter(genus != "g__")
genus_summary %>%
filter(!is.na(relabun)) %>%
group_by(genus) %>%
summarise(mean=mean(relabun),sd=sd(relabun)) %>%
arrange(-mean) %>%
tt()| genus | mean | sd |
|---|---|---|
| g__Bacteroides | 1.492633e-01 | 9.145770e-02 |
| g__Parabacteroides | 6.838309e-02 | 3.825177e-02 |
| g__Phocaeicola | 5.590755e-02 | 4.767695e-02 |
| g__Odoribacter | 3.698228e-02 | 3.157692e-02 |
| g__Alistipes | 3.688633e-02 | 3.262665e-02 |
| g__Kineothrix | 3.485495e-02 | 7.746321e-02 |
| g__JAAYNV01 | 3.180220e-02 | 5.544362e-02 |
| g__Roseburia | 2.034157e-02 | 6.055895e-02 |
| g__Acetatifactor | 1.353817e-02 | 2.662322e-02 |
| g__Ventrimonas | 1.119879e-02 | 1.784188e-02 |
| g__CAG-95 | 1.116264e-02 | 2.245897e-02 |
| g__Helicobacter_J | 1.041623e-02 | 1.995870e-02 |
| g__Parabacteroides_B | 9.901565e-03 | 1.173939e-02 |
| g__Breznakia | 9.810792e-03 | 2.108634e-02 |
| g__Mycoplasmoides | 9.198005e-03 | 1.988191e-02 |
| g__Akkermansia | 7.557137e-03 | 1.368902e-02 |
| g__Velocimicrobium | 7.454088e-03 | 1.907730e-02 |
| g__RGIG4733 | 7.157888e-03 | 2.514900e-02 |
| g__Hungatella_A | 6.350838e-03 | 9.898917e-03 |
| g__UBA866 | 5.974162e-03 | 1.279000e-02 |
| g__Desulfovibrio | 5.709603e-03 | 9.315901e-03 |
| g__Anaerotruncus | 5.630278e-03 | 7.811119e-03 |
| g__Thomasclavelia | 5.493662e-03 | 1.248939e-02 |
| g__Intestinimonas | 5.301231e-03 | 6.478704e-03 |
| g__Bilophila | 5.134848e-03 | 6.647822e-03 |
| g__Ruthenibacterium | 4.907256e-03 | 9.923689e-03 |
| g__Enterocloster | 4.615640e-03 | 6.281140e-03 |
| g__JALFVM01 | 4.503361e-03 | 1.060918e-02 |
| g__Vibrio | 4.421724e-03 | 1.848524e-02 |
| g__Hespellia | 4.402515e-03 | 1.129796e-02 |
| g__Fimenecus | 4.242280e-03 | 1.435771e-02 |
| g__14-2 | 3.563480e-03 | 1.647062e-02 |
| g__Clostridium_Q | 3.535110e-03 | 4.975653e-03 |
| g__NHYM01 | 3.532146e-03 | 9.913909e-03 |
| g__Spiro-02 | 3.529054e-03 | 2.160118e-02 |
| g__Aquirickettsiella | 3.505108e-03 | 4.590552e-02 |
| g__Copromonas | 3.447747e-03 | 4.581581e-03 |
| g__Lawsonibacter | 3.443311e-03 | 5.211912e-03 |
| g__Egerieousia | 3.368690e-03 | 8.602302e-03 |
| g__Protoclostridium | 3.296536e-03 | 2.553531e-02 |
| g__Enterobacter | 3.191565e-03 | 1.402631e-02 |
| g__Lacrimispora | 3.189242e-03 | 7.287909e-03 |
| g__Oscillibacter | 3.157271e-03 | 4.419607e-03 |
| g__CHH4-2 | 3.075367e-03 | 5.253794e-03 |
| g__Escherichia | 3.000053e-03 | 1.115703e-02 |
| g__Limiplasma | 2.969019e-03 | 7.133192e-03 |
| g__Rikenella | 2.939128e-03 | 6.055218e-03 |
| g__Sarcina | 2.877939e-03 | 1.630802e-02 |
| g__CAZU01 | 2.870401e-03 | 4.887287e-03 |
| g__Fusobacterium_A | 2.859566e-03 | 1.339771e-02 |
| g__Dielma | 2.815223e-03 | 6.874781e-03 |
| g__OM05-12 | 2.791990e-03 | 5.749748e-03 |
| g__Phascolarctobacterium | 2.551799e-03 | 4.905513e-03 |
| g__Fimivivens | 2.467945e-03 | 3.688432e-03 |
| g__MGBC136627 | 2.446550e-03 | 6.005822e-03 |
| g__MGBC143606 | 2.440758e-03 | 7.414283e-03 |
| g__Methanimicrococcus | 2.372541e-03 | 9.727454e-03 |
| g__Intestinibacillus | 2.365302e-03 | 5.280365e-03 |
| g__Hungatella | 2.292660e-03 | 4.692286e-03 |
| g__Mailhella | 2.254541e-03 | 3.960166e-03 |
| g__Pseudoflavonifractor | 2.140159e-03 | 5.519017e-03 |
| g__Gemmiger | 2.112060e-03 | 6.521526e-03 |
| g__MGBC140009 | 2.031711e-03 | 5.716638e-03 |
| g__Lachnotalea | 2.012696e-03 | 5.442239e-03 |
| g__Pelethenecus | 2.008513e-03 | 8.013717e-03 |
| g__WRDF01 | 1.983926e-03 | 3.923816e-03 |
| g__MGBC131033 | 1.973766e-03 | 3.165900e-03 |
| g__Dysosmobacter | 1.947698e-03 | 2.768625e-03 |
| g__Negativibacillus | 1.942876e-03 | 4.332910e-03 |
| g__Coprobacillus | 1.934097e-03 | 3.859945e-03 |
| g__Angelakisella | 1.884111e-03 | 3.631754e-03 |
| g__RGIG6463 | 1.836103e-03 | 3.631321e-03 |
| g__MGBC165282 | 1.805128e-03 | 4.854526e-03 |
| g__Buttiauxella | 1.783363e-03 | 6.842193e-03 |
| g__JAAYQI01 | 1.771220e-03 | 3.100609e-03 |
| g__Limenecus | 1.757957e-03 | 3.763048e-03 |
| g__Aeromonas | 1.724892e-03 | 1.089339e-02 |
| g__Agathobaculum | 1.691308e-03 | 3.310944e-03 |
| g__Citrobacter | 1.678009e-03 | 7.050371e-03 |
| g__Coproplasma | 1.676723e-03 | 9.512497e-03 |
| g__SZUA-378 | 1.657792e-03 | 1.399271e-02 |
| g__Bacteroides_E | 1.646079e-03 | 2.158813e-02 |
| g__Eisenbergiella | 1.567253e-03 | 3.864070e-03 |
| g__Acaricomes | 1.546507e-03 | 1.907650e-02 |
| g__SIG332 | 1.531952e-03 | 9.459875e-03 |
| g__CAG-269 | 1.410352e-03 | 3.725174e-03 |
| g__SIG299 | 1.380919e-03 | 7.119758e-03 |
| g__NSJ-61 | 1.352789e-03 | 4.082352e-03 |
| g__RGIG3002 | 1.316711e-03 | 4.431909e-03 |
| g__Marseille-P3106 | 1.288557e-03 | 2.227308e-03 |
| g__WRHT01 | 1.286176e-03 | 3.892975e-03 |
| g__Kosakonia | 1.279803e-03 | 1.185315e-02 |
| g__Emergencia | 1.251317e-03 | 4.473343e-03 |
| g__UMGS1251 | 1.238852e-03 | 3.182570e-03 |
| g__Tidjanibacter | 1.233090e-03 | 3.465801e-03 |
| g__C-19 | 1.222456e-03 | 4.824577e-03 |
| g__Clostridium | 1.193805e-03 | 7.940942e-03 |
| g__Butyricimonas | 1.175332e-03 | 2.982029e-03 |
| g__MGBC116941 | 1.143994e-03 | 4.759873e-03 |
| g__Anaerotignum | 1.131763e-03 | 1.921774e-03 |
| g__Evtepia | 1.125245e-03 | 2.346285e-03 |
| g__Scatousia | 1.113860e-03 | 3.186063e-03 |
| g__Scandinavium | 1.110443e-03 | 1.289658e-02 |
| g__CALTSX01 | 1.109162e-03 | 1.125643e-02 |
| g__Anaeroplasma | 1.099325e-03 | 4.010838e-03 |
| g__UBA2658 | 1.093757e-03 | 2.645590e-03 |
| g__Blautia_A | 1.062518e-03 | 2.897013e-03 |
| g__Proteus | 1.058683e-03 | 1.335374e-02 |
| g__Ruminococcus_E | 1.029855e-03 | 6.336954e-03 |
| g__JAHHSE01 | 1.016881e-03 | 2.081230e-03 |
| g__Anaerostipes | 9.993568e-04 | 6.214220e-03 |
| g__CAJLXD01 | 9.907104e-04 | 2.932215e-03 |
| g__Phocaeicola_A | 9.892770e-04 | 4.013536e-03 |
| g__Fournierella | 9.581274e-04 | 2.619171e-03 |
| g__CAG-345 | 9.417628e-04 | 4.156477e-03 |
| g__Brevinema | 8.957611e-04 | 4.643777e-03 |
| g__Harryflintia | 8.884142e-04 | 2.505438e-03 |
| g__C-53 | 8.874160e-04 | 4.469056e-03 |
| g__Acutalibacter | 8.861698e-04 | 1.776887e-03 |
| g__Aminipila | 8.810006e-04 | 2.463410e-03 |
| g__Spyradomonas | 8.525628e-04 | 4.191135e-03 |
| g__Ventrenecus | 8.497155e-04 | 2.794178e-03 |
| g__CAG-273 | 8.444700e-04 | 4.049118e-03 |
| g__Caccovivens | 8.366088e-04 | 2.621483e-03 |
| g__VSOB01 | 8.152912e-04 | 3.184675e-03 |
| g__CAG-1782 | 7.959184e-04 | 3.106148e-03 |
| g__RGIG1896 | 7.925359e-04 | 1.323233e-03 |
| g__Ruminiclostridium_E | 7.797273e-04 | 3.917287e-03 |
| g__CAG-582 | 7.735000e-04 | 4.481513e-03 |
| g__Blautia | 7.711825e-04 | 1.670642e-03 |
| g__Klebsiella | 7.596956e-04 | 3.591632e-03 |
| g__Bariatricus | 7.585807e-04 | 1.661520e-03 |
| g__Extibacter | 7.391720e-04 | 1.570615e-03 |
| g__Stoquefichus | 7.391191e-04 | 3.131298e-03 |
| g__CALURL01 | 7.372695e-04 | 2.459028e-03 |
| g__JAAWBF01 | 7.270628e-04 | 2.291304e-03 |
| g__UBA1436 | 7.244074e-04 | 2.911088e-03 |
| g__UBA5578 | 6.989678e-04 | 4.423923e-03 |
| g__IOR16 | 6.837972e-04 | 1.623524e-03 |
| g__CAG-288 | 6.814792e-04 | 2.646198e-03 |
| g__Clostridium_AI | 6.796597e-04 | 7.646021e-03 |
| g__MGBC133411 | 6.731026e-04 | 1.995666e-03 |
| g__CALUVN01 | 6.547298e-04 | 1.647970e-03 |
| g__Scatenecus | 6.527575e-04 | 2.463681e-03 |
| g__UBA7185 | 6.237137e-04 | 2.850324e-03 |
| g__Faecousia | 6.199737e-04 | 2.757282e-03 |
| g__Muricomes | 6.193494e-04 | 2.526333e-03 |
| g__Scatacola_A | 6.113889e-04 | 2.209083e-03 |
| g__Faecalibacillus | 6.073162e-04 | 3.608509e-03 |
| g__Harrysmithimonas | 6.063947e-04 | 2.890469e-03 |
| g__CAJTFG01 | 5.848933e-04 | 3.604164e-03 |
| g__Bacilliculturomica | 5.704876e-04 | 1.402287e-03 |
| g__Faecisoma | 5.592534e-04 | 2.521527e-03 |
| g__Methanocorpusculum | 5.525498e-04 | 2.600043e-03 |
| g__Anaerocaecibacter | 5.522731e-04 | 2.721369e-03 |
| g__CAKQDS01 | 5.418129e-04 | 2.199150e-03 |
| g__Salmonella | 5.276877e-04 | 4.414352e-03 |
| g__RGIG8482 | 5.219404e-04 | 1.949521e-03 |
| g__Galloscillospira_A | 5.158552e-04 | 9.715988e-04 |
| g__Fimivicinus | 5.153979e-04 | 2.165963e-03 |
| g__Fimimorpha | 4.980684e-04 | 2.338325e-03 |
| g__JAGAJR01 | 4.971561e-04 | 3.285758e-03 |
| g__Caccenecus | 4.949970e-04 | 1.527726e-03 |
| g__UBA1794 | 4.933027e-04 | 1.707288e-03 |
| g__UBA1417 | 4.791205e-04 | 1.029684e-03 |
| g__UBA940 | 4.740035e-04 | 1.712347e-03 |
| g__CAJFPI01 | 4.629136e-04 | 1.001336e-03 |
| g__Lactonifactor | 4.603409e-04 | 1.417494e-03 |
| g__Clostridium_AQ | 4.466972e-04 | 1.736532e-03 |
| g__Onthovicinus | 4.445381e-04 | 2.331257e-03 |
| g__Buchnera | 4.433102e-04 | 5.813959e-03 |
| g__Clostridium_N | 4.402910e-04 | 2.950622e-03 |
| g__CAKRHR01 | 4.367869e-04 | 2.278772e-03 |
| g__DXYV01 | 4.360731e-04 | 1.398616e-03 |
| g__RGIG1902 | 4.283551e-04 | 7.371513e-04 |
| g__SIG32 | 4.227733e-04 | 1.529877e-03 |
| g__HGM11386 | 4.218531e-04 | 1.727808e-03 |
| g__Butyrivibrio_A | 4.136198e-04 | 3.448206e-03 |
| g__FLUQ01 | 4.120756e-04 | 9.918380e-04 |
| g__CAG-590 | 4.073011e-04 | 1.856155e-03 |
| g__Faecimonas | 4.024457e-04 | 1.952064e-03 |
| g__MGBC107952 | 4.009827e-04 | 1.132923e-03 |
| g__Ventrisoma | 3.996970e-04 | 1.047519e-03 |
| g__Beduini | 3.891743e-04 | 1.496954e-03 |
| g__RUG14156 | 3.667219e-04 | 1.782969e-03 |
| g__Cloacibacillus | 3.666072e-04 | 2.431173e-03 |
| g__Pseudomonas | 3.626249e-04 | 2.913546e-03 |
| g__Lawsonia | 3.609631e-04 | 2.976114e-03 |
| g__Marvinbryantia | 3.602193e-04 | 1.589621e-03 |
| g__CAG-465 | 3.584980e-04 | 1.153031e-03 |
| g__Coprobacter | 3.568144e-04 | 1.332767e-03 |
| g__HGM12998 | 3.510965e-04 | 1.268564e-03 |
| g__Faecenecus | 3.477335e-04 | 1.547966e-03 |
| g__RACS-047 | 3.410345e-04 | 1.305915e-03 |
| g__RGIG4097 | 3.394551e-04 | 2.512766e-03 |
| g__CAG-303 | 3.354250e-04 | 2.253817e-03 |
| g__Paraeggerthella | 3.306477e-04 | 7.881768e-04 |
| g__Scatavimonas | 3.292069e-04 | 2.998578e-03 |
| g__Scatocola | 3.170079e-04 | 2.010498e-03 |
| g__CAKTEE01 | 3.148626e-04 | 1.817047e-03 |
| g__UBA7488 | 3.139388e-04 | 1.531614e-03 |
| g__Caccomorpha | 3.135442e-04 | 8.132352e-04 |
| g__UBA710 | 3.110466e-04 | 3.810180e-03 |
| g__Gallibacteroides | 3.095362e-04 | 9.740463e-04 |
| g__Lachnospira | 3.070567e-04 | 1.867816e-03 |
| g__CALXUC01 | 3.067121e-04 | 1.882934e-03 |
| g__JAIHAL01 | 2.938058e-04 | 1.765062e-03 |
| g__Zag111 | 2.895640e-04 | 1.695054e-03 |
| g__Ventricola | 2.878743e-04 | 1.507071e-03 |
| g__Scatomorpha | 2.765635e-04 | 7.278705e-04 |
| g__Lachnoclostridium_B | 2.763740e-04 | 8.906298e-04 |
| g__UBA5026 | 2.752265e-04 | 1.128502e-03 |
| g__Caccosoma | 2.706635e-04 | 1.015132e-03 |
| g__Catenibacillus | 2.681525e-04 | 7.308965e-04 |
| g__JAGBWK01 | 2.667486e-04 | 2.985884e-03 |
| g__RGIG4057 | 2.634560e-04 | 1.610134e-03 |
| g__Oliverpabstia | 2.606026e-04 | 2.224448e-03 |
| g__UMGS1202 | 2.590747e-04 | 8.409060e-04 |
| g__HGM05232 | 2.559188e-04 | 7.315989e-04 |
| g__Merdicola | 2.528427e-04 | 1.910082e-03 |
| g__Cryptoclostridium | 2.450743e-04 | 1.574707e-03 |
| g__UMGS2016 | 2.439149e-04 | 1.057064e-03 |
| g__CALXWF01 | 2.437349e-04 | 8.980698e-04 |
| g__Onthocola_B | 2.336122e-04 | 1.097069e-03 |
| g__RUG14670 | 2.334104e-04 | 1.268072e-03 |
| g__UMGS1663 | 2.320796e-04 | 1.174466e-03 |
| g__Plesiomonas | 2.292023e-04 | 2.122607e-03 |
| g__SIG230 | 2.280915e-04 | 9.725989e-04 |
| g__Butyricicoccus | 2.280100e-04 | 1.179904e-03 |
| g__Butyribacter | 2.278963e-04 | 1.554091e-03 |
| g__HGM13233 | 2.269566e-04 | 1.044833e-03 |
| g__JAHHUA01 | 2.254978e-04 | 1.219591e-03 |
| g__CALWZU01 | 2.244363e-04 | 7.795409e-04 |
| g__CAG-977 | 2.225261e-04 | 1.355731e-03 |
| g__Aphodocola | 2.222897e-04 | 1.161474e-03 |
| g__CALXRO01 | 2.218957e-04 | 1.970482e-03 |
| g__Heteroruminococcus | 2.202694e-04 | 9.244284e-04 |
| g__JAJQAW01 | 2.169416e-04 | 7.681528e-04 |
| g__Onthenecus | 2.147993e-04 | 1.115093e-03 |
| g__RGIG7389 | 2.135590e-04 | 6.700920e-04 |
| g__Faecivivens | 2.124632e-04 | 6.117535e-04 |
| g__Onthousia | 2.092884e-04 | 1.156334e-03 |
| g__SIG350 | 2.069507e-04 | 2.714132e-03 |
| g__Zhenpiania | 2.019229e-04 | 4.491625e-04 |
| g__WQYD01 | 2.010363e-04 | 7.107867e-04 |
| g__Schmidhempelia | 1.993159e-04 | 2.428842e-03 |
| g__CAJKWP01 | 1.983903e-04 | 1.179880e-03 |
| g__Enterococcus_B | 1.954034e-04 | 9.681045e-04 |
| g__JAILHT01 | 1.916321e-04 | 1.904125e-03 |
| g__RGIG3701 | 1.908305e-04 | 1.714429e-03 |
| g__Ignatzschineria | 1.894434e-04 | 2.484527e-03 |
| g__Avoscillospira_A | 1.849958e-04 | 7.621367e-04 |
| g__RUG12867 | 1.830035e-04 | 9.744369e-04 |
| g__CAG-245 | 1.810191e-04 | 1.094579e-03 |
| g__Anaerovorax | 1.807911e-04 | 8.302159e-04 |
| g__Raoultibacter | 1.797664e-04 | 8.292516e-04 |
| g__UMGS1585 | 1.752553e-04 | 7.702768e-04 |
| g__Oxalobacter | 1.721286e-04 | 7.779434e-04 |
| g__Hafnia | 1.709747e-04 | 1.378637e-03 |
| g__CAG-510 | 1.665191e-04 | 8.640457e-04 |
| g__Kluyvera | 1.663693e-04 | 1.308586e-03 |
| g__Hepatoplasma | 1.654048e-04 | 1.179092e-03 |
| g__UMGS75 | 1.626765e-04 | 1.435280e-03 |
| g__JADFUS01 | 1.619273e-04 | 6.573895e-04 |
| g__UBA7405 | 1.612771e-04 | 2.016590e-03 |
| g__Streptococcus | 1.564224e-04 | 2.051461e-03 |
| g__CAG-56 | 1.525484e-04 | 6.872474e-04 |
| g__CCUG-7971 | 1.523791e-04 | 6.252194e-04 |
| g__Barb7 | 1.520997e-04 | 1.994769e-03 |
| g__Gallispira | 1.502610e-04 | 1.952849e-03 |
| g__Lapidilactobacillus | 1.409595e-04 | 1.848667e-03 |
| g__Butyricicoccus_A | 1.367025e-04 | 7.053366e-04 |
| g__Limousia | 1.360041e-04 | 6.955315e-04 |
| g__Galligastranaerophilus | 1.353461e-04 | 7.910321e-04 |
| g__RGIG8607 | 1.330395e-04 | 8.153357e-04 |
| g__Romboutsia_C | 1.324145e-04 | 8.281891e-04 |
| g__Enterococcus | 1.324071e-04 | 8.356372e-04 |
| g__Lactococcus_A | 1.314638e-04 | 1.483600e-03 |
| g__Leclercia | 1.312203e-04 | 8.697175e-04 |
| g__Pelethosoma | 1.307797e-04 | 6.745119e-04 |
| g__Lactococcus | 1.281579e-04 | 7.899264e-04 |
| g__MGBC124762 | 1.275812e-04 | 3.998533e-04 |
| g__MGBC102946 | 1.258646e-04 | 5.024944e-04 |
| g__CALXDZ01 | 1.242807e-04 | 4.083501e-04 |
| g__Alectryocaccomicrobium | 1.235486e-04 | 7.824254e-04 |
| g__Avelusimicrobium | 1.231087e-04 | 5.021372e-04 |
| g__Murimonas | 1.213808e-04 | 6.752085e-04 |
| g__CALXIC01 | 1.201073e-04 | 4.762615e-04 |
| g__Eubacterium_R | 1.155168e-04 | 6.661566e-04 |
| g__CAJMNU01 | 1.144585e-04 | 4.126897e-04 |
| g__Metalachnospira | 1.123175e-04 | 3.821465e-04 |
| g__MGBC162267 | 1.119052e-04 | 5.900730e-04 |
| g__JAEXFV01 | 1.108700e-04 | 5.225033e-04 |
| g__UBA4636 | 1.101747e-04 | 5.696311e-04 |
| g__Ruminococcus_G | 1.085800e-04 | 5.727591e-04 |
| g__JAHZFN01 | 1.041903e-04 | 4.947845e-04 |
| g__Alistipes_A | 1.023731e-04 | 3.424616e-04 |
| g__Adamsella | 1.005056e-04 | 8.259359e-04 |
| g__JAAVYW01 | 9.886611e-05 | 3.596087e-04 |
| g__UBA6345 | 9.776278e-05 | 5.890564e-04 |
| g__UMGS1601 | 9.678895e-05 | 1.027188e-03 |
| g__UMGS946 | 9.645721e-05 | 7.355573e-04 |
| g__Catellicoccus | 9.608682e-05 | 8.591908e-04 |
| g__Novisyntrophococcus | 9.472371e-05 | 6.442503e-04 |
| g__CAG-41 | 9.123793e-05 | 6.894142e-04 |
| g__CAG-307 | 9.056080e-05 | 6.397842e-04 |
| g__CAKPCJ01 | 8.942488e-05 | 4.738890e-04 |
| g__JAEWLZ01 | 8.871037e-05 | 1.125625e-03 |
| g__Scybalousia | 8.811278e-05 | 6.607347e-04 |
| g__JAGZHZ01 | 8.729754e-05 | 5.699666e-04 |
| g__Vagococcus | 8.701072e-05 | 1.141135e-03 |
| g__CAG-177 | 8.598892e-05 | 6.008884e-04 |
| g__JALENY01 | 8.400275e-05 | 7.456506e-04 |
| g__UBA1234 | 8.317669e-05 | 3.789843e-04 |
| g__Eggerthella | 8.252648e-05 | 3.589205e-04 |
| g__Paraclostridium | 8.049454e-05 | 6.908705e-04 |
| g__UBA9414 | 7.948449e-05 | 4.143991e-04 |
| g__Howiella | 7.930957e-05 | 4.148145e-04 |
| g__WRAV01 | 7.609451e-05 | 3.151892e-04 |
| g__1XD8-76 | 7.561457e-05 | 5.115263e-04 |
| g__Coprosoma | 7.472227e-05 | 3.452372e-04 |
| g__Symbiothrix | 7.440778e-05 | 9.758489e-04 |
| g__Eubacterium_F | 7.419399e-05 | 4.473563e-04 |
| g__CALVUN01 | 7.360091e-05 | 2.973254e-04 |
| g__SIG471 | 7.262934e-05 | 2.760627e-04 |
| g__PeH17 | 7.223390e-05 | 6.588230e-04 |
| g__CALVXC01 | 7.196506e-05 | 6.695435e-04 |
| g__RGIG4709 | 6.834702e-05 | 3.413827e-04 |
| g__NSJ-51 | 6.807371e-05 | 2.871386e-04 |
| g__Stercorousia | 6.781125e-05 | 5.448313e-04 |
| g__Gordonibacter | 6.717435e-05 | 2.612900e-04 |
| g__MGBC114844 | 6.659331e-05 | 4.105335e-04 |
| g__Pelethomonas | 6.618416e-05 | 2.448069e-04 |
| g__Victivallis | 6.489695e-05 | 4.051890e-04 |
| g__RGIG9115 | 6.478642e-05 | 4.986757e-04 |
| g__UBA1405 | 6.337712e-05 | 3.647934e-04 |
| g__MGBC164599 | 6.309143e-05 | 2.415782e-04 |
| g__UMGS1754 | 6.307099e-05 | 4.707822e-04 |
| g__CAG-196 | 6.303657e-05 | 3.691902e-04 |
| g__Fructobacillus | 6.009139e-05 | 7.880912e-04 |
| g__Anaeromassilibacillus | 5.991756e-05 | 4.100453e-04 |
| g__MGBC120314 | 5.725195e-05 | 5.476452e-04 |
| g__JAAZGC01 | 5.557462e-05 | 5.355315e-04 |
| g__CAG-314 | 5.351060e-05 | 4.224425e-04 |
| g__Cellulosilyticum | 5.332328e-05 | 3.808652e-04 |
| g__Enterousia | 5.188415e-05 | 4.191287e-04 |
| g__UMGS687 | 5.126641e-05 | 4.219539e-04 |
| g__Erysipelothrix | 5.024616e-05 | 6.589722e-04 |
| g__Holdemania | 4.990583e-05 | 2.392481e-04 |
| g__Limivicinus | 4.957042e-05 | 6.142188e-04 |
| g__RGIG4790 | 4.884680e-05 | 4.322050e-04 |
| g__Enterococcus_D | 4.788989e-05 | 4.103756e-04 |
| g__UBA933 | 4.778105e-05 | 6.266426e-04 |
| g__Copranaerobaculum | 4.777314e-05 | 2.215807e-04 |
| g__SIG603 | 4.629171e-05 | 3.498294e-04 |
| g__CAKVBE01 | 4.606653e-05 | 6.041568e-04 |
| g__Mobilisporobacter | 4.560952e-05 | 4.555415e-04 |
| g__QVMH01 | 4.504653e-05 | 2.212459e-04 |
| g__Hydrogenoanaerobacterium | 4.475602e-05 | 1.749987e-04 |
| g__CALWRB01 | 4.428930e-05 | 1.565875e-04 |
| g__HGM16780 | 4.234877e-05 | 3.457660e-04 |
| g__JAFSEX01 | 4.208347e-05 | 5.006300e-04 |
| g__CALWTV01 | 4.031353e-05 | 4.868653e-04 |
| g__Ruminococcus | 4.026239e-05 | 5.280363e-04 |
| g__Providencia | 3.947092e-05 | 4.865493e-04 |
| g__Woodwardibium | 3.918633e-05 | 1.936551e-04 |
| g__Frigididesulfovibrio | 3.840477e-05 | 5.036739e-04 |
| g__Wohlfahrtiimonas | 3.820192e-05 | 5.010134e-04 |
| g__Eubacterium | 3.408400e-05 | 1.552477e-04 |
| g__Morganella | 3.398929e-05 | 4.457653e-04 |
| g__Enterococcus_J | 3.334065e-05 | 4.372585e-04 |
| g__Neoruminococcus | 3.310136e-05 | 1.689688e-04 |
| g__RUG13868 | 3.198945e-05 | 2.291845e-04 |
| g__UBA1394 | 3.162426e-05 | 2.289144e-04 |
| g__JAAZDN01 | 3.052698e-05 | 4.003575e-04 |
| g__CAG-452 | 2.832554e-05 | 1.923112e-04 |
| g__Paracoccus | 2.776073e-05 | 3.101775e-04 |
| g__JAILQS01 | 2.736465e-05 | 1.827364e-04 |
| g__CAKNOI01 | 2.732478e-05 | 3.262900e-04 |
| g__RGIG2219 | 2.626128e-05 | 1.876693e-04 |
| g__CAJOJR01 | 2.582848e-05 | 2.076085e-04 |
| g__Ventrousia | 2.576615e-05 | 1.230955e-04 |
| g__HGM13862 | 2.435275e-05 | 9.859687e-05 |
| g__Methanoplasma | 2.278412e-05 | 2.988110e-04 |
| g__Heteroclostridium | 2.072692e-05 | 1.253234e-04 |
| g__RGIG5057 | 2.033912e-05 | 1.439685e-04 |
| g__Heteroscilispira | 2.015044e-05 | 1.254733e-04 |
| g__RGIG3091 | 1.786547e-05 | 2.343035e-04 |
| g__RGIG446 | 1.709062e-05 | 8.960743e-05 |
| g__Lentilactobacillus | 1.631166e-05 | 2.139254e-04 |
| g__Microbacterium | 1.467237e-05 | 1.924263e-04 |
| g__Alloscillospira | 1.272669e-05 | 1.020529e-04 |
| g__CALXXL01 | 1.228690e-05 | 7.294195e-05 |
| g__SIG208 | 6.550316e-06 | 5.024769e-05 |
| g__CAKVLS01 | 6.485638e-06 | 5.776699e-05 |
| g__JAGVVH01 | 5.663380e-06 | 7.427454e-05 |
genus_arrange <- genus_summary %>%
group_by(genus) %>%
summarise(mean=sum(relabun)) %>%
filter(genus != "g__")%>%
arrange(-mean) %>%
select(genus) %>%
mutate(genus= sub("^g__", "", genus)) %>%
pull()
genus_summary %>%
left_join(genome_metadata_all %>% select(genus,phylum) %>% unique(),by=join_by(genus==genus)) %>%
left_join(sample_metadata_all,by=join_by(sample==sample)) %>%
mutate(genus= sub("^g__", "", genus)) %>%
filter(genus %in% genus_arrange[1:20]) %>%
mutate(genus=factor(genus,levels=rev(genus_arrange[1:20]))) %>%
filter(relabun > 0) %>%
ggplot(aes(x=relabun, y=genus, group=genus, color=phylum)) +
scale_color_manual(values=phylum_colors_all) +
#geom_boxplot() +
geom_jitter(alpha=0.5) +
facet_nested(. ~ species)+
theme_minimal()5.3 Compositional dissimilarities
beta_q0n <- genome_counts_filt_all %>%
column_to_rownames(., "genome") %>%
filter(rowSums(. != 0, na.rm = TRUE) > 0) %>%
select_if(~!all(. == 0)) %>%
hillpair(., q = 0)
beta_q1n <- genome_counts_filt_all %>%
column_to_rownames(., "genome") %>%
filter(rowSums(. != 0, na.rm = TRUE) > 0) %>%
select_if(~!all(. == 0)) %>%
hillpair(., q = 1)
beta_q1p <- genome_counts_filt_all %>%
column_to_rownames(., "genome") %>%
filter(rowSums(. != 0, na.rm = TRUE) > 0) %>%
select_if(~!all(. == 0)) %>%
hillpair(., q = 1, tree = genome_tree_all)5.3.1 Richness dissimilarity plot
nmds_q0n <- beta_q0n$S %>%
vegan::metaMDS(., trymax = 500, k = 2, trace=0) %>%
vegan::scores() %>%
as_tibble(., rownames = "sample") %>%
dplyr::left_join(sample_metadata_all, by = "sample") %>%
group_by(species,population) %>%
mutate(x_cen = mean(NMDS1, na.rm = TRUE)) %>%
mutate(y_cen = mean(NMDS2, na.rm = TRUE)) %>%
ungroup()
nmds_q0n %>%
ggplot(aes(x = NMDS1, y = NMDS2, color = species, fill = species, shape = population_type)) +
geom_point(size = 2) +
scale_color_manual(values=c("#f48153","#83d3d4","#2d8183","#910c07"))+
# stat_ellipse(aes(color = beta_q1n_nmds$Groups))+
geom_segment(aes(x = x_cen, y = y_cen, xend = NMDS1, yend = NMDS2), alpha = 0.5) +
theme_classic() +
theme(
axis.text.x = element_text(size = 12),
axis.text.y = element_text(size = 12),
axis.title = element_text(size = 20, face = "bold"),
axis.text = element_text(face = "bold", size = 18),
panel.background = element_blank(),
axis.line = element_line(size = 0.5, linetype = "solid", colour = "black"),
legend.text = element_text(size = 16),
legend.title = element_text(size = 18),
legend.position = "right", legend.box = "vertical"
) +
labs(shape="Population type",color="Species",fill="Species")5.3.2 Neutral diversity dissimilarity plot
nmds_q1n <- beta_q1n$S %>%
vegan::metaMDS(., trymax = 500, k = 2, trace=0) %>%
vegan::scores() %>%
as_tibble(., rownames = "sample") %>%
dplyr::left_join(sample_metadata_all, by = "sample") %>%
group_by(species,population) %>%
mutate(x_cen = mean(NMDS1, na.rm = TRUE)) %>%
mutate(y_cen = mean(NMDS2, na.rm = TRUE)) %>%
ungroup()
nmds_q1n %>%
ggplot(aes(x = NMDS1, y = NMDS2, color = species, fill = species, shape = population_type)) +
geom_point(size = 2) +
scale_color_manual(values=c("#f48153","#83d3d4","#2d8183","#910c07"))+
# stat_ellipse(aes(color = beta_q1n_nmds$Groups))+
geom_segment(aes(x = x_cen, y = y_cen, xend = NMDS1, yend = NMDS2), alpha = 0.5) +
theme_classic() +
theme(
axis.text.x = element_text(size = 12),
axis.text.y = element_text(size = 12),
axis.title = element_text(size = 20, face = "bold"),
axis.text = element_text(face = "bold", size = 18),
panel.background = element_blank(),
axis.line = element_line(size = 0.5, linetype = "solid", colour = "black"),
legend.text = element_text(size = 16),
legend.title = element_text(size = 18),
legend.position = "right", legend.box = "vertical"
) +
labs(shape="Population type",color="Species",fill="Species")5.3.3 Phylogenetic diversity dissimilarity plot
nmds_q1p <- beta_q1p$S %>%
vegan::metaMDS(., trymax = 500, k = 2, trace=0) %>%
vegan::scores() %>%
as_tibble(., rownames = "sample") %>%
dplyr::left_join(sample_metadata_all, by = "sample") %>%
group_by(species,population) %>%
mutate(x_cen = mean(NMDS1, na.rm = TRUE)) %>%
mutate(y_cen = mean(NMDS2, na.rm = TRUE)) %>%
ungroup()
nmds_q1p %>%
ggplot(aes(x = NMDS1, y = NMDS2, color = species, fill = species, shape = population_type)) +
geom_point(size = 2) +
scale_color_manual(values=c("#f48153","#83d3d4","#2d8183","#910c07"))+
# stat_ellipse(aes(color = beta_q1n_nmds$Groups))+
geom_segment(aes(x = x_cen, y = y_cen, xend = NMDS1, yend = NMDS2), alpha = 0.5) +
theme_classic() +
theme(
axis.text.x = element_text(size = 12),
axis.text.y = element_text(size = 12),
axis.title = element_text(size = 20, face = "bold"),
axis.text = element_text(face = "bold", size = 18),
panel.background = element_blank(),
axis.line = element_line(size = 0.5, linetype = "solid", colour = "black"),
legend.text = element_text(size = 16),
legend.title = element_text(size = 18),
legend.position = "right", legend.box = "vertical"
) +
labs(shape="Population type",color="Species",fill="Species")